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snakemake_notes's Introduction

Snakemake_Notes

Why use Snakemake?

  • Preservation is easier
  • Built on top of python
  • Easy to implement docker, conda, and tagged versions
  • Supports batch jobs and parllelization

Snakefile

  • Stores rules for building intermediate items (input, output, command)
  • Inputs are outputs of other rules
  • rules.[rulename].output_file can be used to refer to the output of a specific rule
  • expand wildcard allows you to expand out a variable

Notes from Mike Love

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